From c9def4631ced0e06c4c10bbbc84d7e7fe313f91b Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 14 Dec 2017 15:53:53 +0100 Subject: changed info text rebuilding models --- views/info.haml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/views/info.haml b/views/info.haml index 34ded87..d8b93f9 100644 --- a/views/info.haml +++ b/views/info.haml @@ -1,2 +1,2 @@ %div.info - currently no models available + We are rebuilding the models. It will take a while, please be patient and reload the page in some time. -- cgit v1.2.3 From 245a13f5e8e887ea0884eebe15845b8d768b1e71 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 20 Mar 2018 16:57:19 +0100 Subject: updated faq and qmrf report --- FAQ.md | 24 ++++++++++++++++++++++-- qmrf_report.rb | 14 +++++++++++++- 2 files changed, 35 insertions(+), 3 deletions(-) diff --git a/FAQ.md b/FAQ.md index 2530968..24283cb 100644 --- a/FAQ.md +++ b/FAQ.md @@ -1,6 +1,6 @@ -## lazar Frequently Asked Questions +## *lazar* Frequently Asked Questions -####The LAZAR program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version, I would consider a confidence value higher than 0.025 as reliable. But now, there is no such parameter in the prediction results. How can I consider a prediction as presenting high or low confidence? +#### The *lazar* program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version, I would consider a confidence value higher than 0.025 as reliable. But now, there is no such parameter in the prediction results. How can I consider a prediction as presenting high or low confidence? In the past many users had problems to interpret the confidence level, for this reason we provide now the probabilities that the prediction @@ -16,3 +16,23 @@ activities of similar compounds. Probabilities are calculated from the activities and similarities of neighbors, please make sure to inspect the neighbors list for any inconsistencies that might affect the prediction. + +#### How can I use *lazar* locally on my computer +If you are familiar with docker, you can use one of our docker images to run lazar locally: +https://hub.docker.com/r/insilicotox/lazar +https://hub.docker.com/r/insilicotox/nano-lazar + +If you want to install lazar/nano-lazar without docker you should know how to use UNIX/Linux and the Ruby programming language. Source code and brief installation instructions for the GUIs is available at: + +https://github.com/opentox/lazar-gui +https://github.com/opentox/nano-lazar + +You can also use just the libraries from the command line: + +https://github.com/opentox/lazar + +Documentation is available at: + +http://www.rubydoc.info/gems/lazar + +lazar depends on a couple of external libraries and programs, that could be difficult to install. Due to limited resources we cannot provide support, please use the docker version if you cannot manage it on your own. diff --git a/qmrf_report.rb b/qmrf_report.rb index b52e618..a031305 100644 --- a/qmrf_report.rb +++ b/qmrf_report.rb @@ -27,10 +27,22 @@ def qmrf_report id # Date of QMRF 2.1 report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}" - # QMRF author(s) and contact details 2.1 + # QMRF author(s) and contact details 2.2 report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor + # Date of QMRF update(s) 2.3 + if prediction_model.name =~ /TD50|multiple/ + report.value "qmrf_date_revision", "2014-12-05" + end + + # Date of QMRF update(s) 2.4 + if prediction_model.name =~ /TD50/ + report.value "qmrf_revision", "Q29-44-39-423" + elsif prediction_model.name =~ /multiple/ + report.value "qmrf_revision", "Q28-43-38-420" + end + # Model developer(s) and contact details 2.5 report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} report.ref_catalog :model_authors, :authors_catalog, :modelauthor -- cgit v1.2.3 From aa678ba1f3988d2b42f372b6da0499b403708e58 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 3 Apr 2018 13:41:15 +0000 Subject: version bump;caret documentation fix --- VERSION | 2 +- lazar-gui.gemspec | 2 +- views/model_details.haml | 9 +++++++-- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/VERSION b/VERSION index 26aaba0..88c5fb8 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.2.0 +1.4.0 diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index 2f40224..104fb29 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -13,7 +13,7 @@ Gem::Specification.new do |s| s.rubyforge_project = "lazar-gui" s.files = `git ls-files`.split("\n") - s.add_runtime_dependency "lazar", ">= 1.0.0" + s.add_runtime_dependency "lazar" s.add_runtime_dependency "sinatra" s.add_runtime_dependency "rdiscount" s.add_runtime_dependency "haml" diff --git a/views/model_details.haml b/views/model_details.haml index d85d2fb..c5e3370 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -28,8 +28,13 @@ = ", min: #{model.model.algorithms["similarity"]["min"]}" %br Prediction: - %a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"} - = model.model.algorithms["prediction"]["method"] + - if model.model.algorithms["prediction"]["method"] !~ /Caret/ + %a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"} + = model.model.algorithms["prediction"]["method"] + - else + %a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox/Algorithm/Caret", :rel=>"external"} + = model.model.algorithms["prediction"]["method"] + %br Descriptors: = model.model.algorithms["descriptors"]["method"]+"," -- cgit v1.2.3 From ca94d4b7e8ad0cab13e66be7a34b0cde21948c69 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 3 Apr 2018 14:24:09 +0000 Subject: follow up master --- VERSION | 2 +- views/predict.haml | 3 ++- views/prediction.haml | 13 ++++++++++++- 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/VERSION b/VERSION index 88c5fb8..f0bb29e 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.4.0 +1.3.0 diff --git a/views/predict.haml b/views/predict.haml index 89bef7c..2308911 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -180,5 +180,6 @@ %h2 3. Predict %div.col-lg-10.col-md-10.col-sm-10.col-xs-10 - %input.btn.btn-warning.h2{ :type => "submit", :id => "submit", :value=>">>", :onclick => "getsmiles()"} + %button.has-feedback.btn.btn-warning.h2{:type => "submit", :id => "submit", :value=>"", :onclick => "getsmiles()"} + %span.glyphicon.glyphicon-play %img.h2{:src=>"/images/wait30trans.gif", :id=>"circle", :class=>"circle", :alt=>"wait", :style=>"display:none;"} diff --git a/views/prediction.haml b/views/prediction.haml index 9cdedde..80b4d16 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -1,3 +1,11 @@ +:javascript + $(document).ready(function(){ + $('[data-toggle="popover"]').popover(); + $('.modal').on('hidden.bs.modal', function () { + $(this).removeData('bs.modal'); + }); + }); + %div.well %a.btn.btn-warning{:href => to('/predict')} %i.glyphicon.glyphicon-menu-left @@ -35,7 +43,10 @@ / show message about dbhit and measurements %p - %b Compound is part of the training dataset + :plain + This compound was part of the training dataset. All information
+ from this compound was removed from the training data before the
+ prediction, to obtain unbiased results. %p %b Measured activity: %br -- cgit v1.2.3